tbuckley/cabot-search huggingface dataset:
BIOL-14. FROM NON-MALIGNANT TO MALIGNANT: GENERATING AND TARGETING DIFFUSE MIDLINE GLIOMA IN A NOVEL HUMAN PONTINE ORGANOID MODEL
Authors: Nils Bessler, Cristian Ruiz Moreno, Amber Wezenaar, Noëlle Dommann, Farid Keramati, Hendrikus C R Ariese, Celina Honhoff, Sam de Blank, Mario Barrera Román, Raphaël Collot, Ravian van Ineveld, Maria Alieva Krashennikova, Mariette E G Kranendonk, Ellen J Wehrens, Anna Alemany, Henk G Stunnenberg, Anne C Rios
Journal: Neuro-Oncology (2023)

Abstract Diffuse Midline Glioma (DMG) is a rare and aggressive pediatric cancer with no chance of survival, demonstrating a critical need for therapy development. Predictive preclinical models that take into account the unique developmental background and anatomical environment of DMG, are so far lacking. We developed a new regionally patterned brain organoid protocol based on a timely regulated sequence of morphogens. The patterned organoids give rise to pontine and medulla oblongata identity, as confirmed by transcriptomic profiling and immunofluorescence imaging. As the tissue matures, the complexity inherently takes shape and gives rise to pons-specific neurons and glial cells, offering the first human in vitro model for this region of the brain. Introducing H3K27M, including its partner mutations P53 and PDGFRA-D842V via electroporation forms de novo H3K27M diffuse midline glioma with a similar genetic make-up as found in patients. Indeed, contrary to common cell lines or PDX models, single cell sequencing and 3D imaging reveal that Organoid-DMG resembles WHO-defined primary patient cancer, including its diverse cell population heterogeneity and invasive nature. Utilizing barcode-based lineage tracing allows us to unravel and track the cancerous developmental evolution. Thus, we can now model early emerging populations and identify their transcriptomic signatures, which is conceptually impossible to conduct with patient-derived tumor tissue. In summary, we generated a bona fide DMG in vitro model which will give insights into tumorigenesis of DMG and ultimately contribute to pre-clinical drug- and immunotherapy development.
BIOL-07. DISTINCTIVE FEATURES OF HIGH-GRADE GLIOMA MOUSE MODELS REVEALED BY SINGLE-NUCLEUS RNA-SEQUENCING GUIDE PRE-CLINICAL MODEL SELECTION
Authors: Kati Ernst, Konstantin Okonechnikov, Laura von Soosten, Nina Hofmann, Norman Mack, Benjamin Schwalm, Robert J Wechsler-Reya, Stefan M Pfister, Supat Thongjuea, David T W Jones, Marc Zuckermann
Journal: Neuro-Oncology (2023)

Abstract Glioma is the most common pediatric central nervous system tumor, with high-grade gliomas (HGG) having one of the worst prognoses of all human cancers. In order to develop better diagnostics and therapies, it is essential to use faithful disease models. Currently, highly passaged patient-derived xenograft (PDX) models are most widely used in preclinical studies, although alternative immunocompetent models are becoming increasingly available. Here, we compare several in vivo glioma models on a single-cell level and investigate their similarity to primary human tumors. Single-nucleus sequencing was used to analyze &amp;gt;125,000 nuclei of primary patient samples, xenografts, autochthonous mouse tumors and related allografts including early and late in vivo passages – with a focus on MET-fusion-driven as well as H3 K27M-mutant HGG. Transcriptomic profiles of single tumor cells and associated stromal/immune components reveal insights into model-specific intratumoral heterogeneity, tumor evolution, and similarities between mouse models and patient samples. In addition, matched tumors engrafted into immunocompromised and immunocompetent animals are used to examine tumor-immune crosstalk and the modifying role of the tumor microenvironment. This improved understanding of how the analyzed model systems evolve over time and how they reflect patient’s tumor compositions will allow to prioritize and refine modern preclinical trials.
METB-05. NON-INVASIVE DIAGNOSIS OF BRAINSTEM GLIOMAS IN PEDIATRIC, ADOLESCENT, AND YOUNG ADULT PATIENTS THROUGH CEREBROSPINAL FLUID CELL-FREE DNA SEQUENCING
Authors: Katherine Hill, Alexandra Giantini-Larsen, Richard A Hickman, Bridget Holle, Tina Alano, Seyram Doe-Tetteh, Nancy Bouvier, Shanita Li, Emily Stockfisch, Claudia Huereca, Sara DiNapoli, Charli Ann Hertz, Alex Lee, Luca Szalontay, Bryan Kincheon Li, Cecile Riviere-Cazaux, Terry C Burns, Sofia Haque, Tejus Bale, Jamal Benhamida, Snjezana Dogan, Chad Vanderbilt, Laetitia Borsu, Dara Ross, Jason Chang, Caroline Barbosa Zampieri, Maria Donzelli, Ira J Dunkel, Kim Kramer, Sameer Farouk Sait, Yasmin Khakoo, Stephen Gilheeney, Mark Souweidane, Jeffery Greenfield, Michael Berger, Maria Arcila, Marc Ladanyi, Ingo Mellinghoff, Matthias Karajannis, Alexandra Miller
Journal: Neuro-Oncology (2023)

Abstract Intrinsic brainstem tumors arising in pediatric, adolescent, and young adult patients comprise a spectrum of entities, predominantly diffuse midline gliomas (DMG) and IDH mutant astrocytomas. Accurate molecular diagnosis is essential for prognostication and optimal therapy. Therapeutic considerations include inclusion (in IDH mutant) or exclusion (in H3K27M) of adjuvant Temozolomide post radiotherapy and use of molecular targeted therapy (IDH inhibitors). Surgical biopsy, however, is associated with increased risk of permanent neurological deficits and may yield insufficient or non-diagnostic tissue. We hypothesized that minimally-invasive “liquid biopsy” of cerebrospinal fluid (CSF) could represent a superior diagnostic modality in this patient population, employing molecular analysis of cell free DNA (cfDNA). We analyzed 44 CSF samples from 38 unique patients for recurrent driver mutations in brainstem gliomas, including H3K27M, IDH1, and IDH2. MSK-IMPACT, a NY state-authorized hybridization capture-based next-generation panel DNA sequencing assay, was used for analysis. Samples without a detectable driver mutation by MSK-IMPACT testing were further subjected to gene targeted testing by droplet digital PCR. In all, 10/44 (22.7%) samples had mutations detected by MSK-IMPACT using standard calling criteria and 13 of the remaining 34 samples (38.2%) had supporting evidence of a mutation based on manual review. Further testing by ddPCR was performed on a subset of cases (based on DNA availability) which confirmed 7 of the previous low-level mutations and uncovered 4 additional mutations. Overall, 27/44 (61.4%) of cases had detectable evidence of a mutation, and of the 23 patients without a known tissue diagnosis, a driver in the CSF was identified for 47.8% of patients (11/23). Minimally-invasive analysis of CSF cfDNA in patients with intrinsic brainstem tumors has a high diagnostic yield and may obviate the need for tissue biopsy in a majority of patients. Testing with high sensitivity assays is valuable to maximize the rate of detection.
MDB-45. SELECTIVE B7-H3 INHIBITORS NI1 AND NI4 REDUCE AGGRESSIVENESS OF GROUP 3 MEDULLOBLASTOMA
Authors: Prakadeeswari Gopala Krishnan, Ranjana Kanchan, David Doss, Hamdan Alfrefaei, Prachi Agarwal, Yashpal Chhonker, D J J Murry, Paul Trippier, Sidharth Mahapatra
Journal: Neuro-Oncology (2023)

Abstract Medulloblastoma (MB) is a primary childhood malignancy of the central nervous system (CNS). Clinically heterogenous MB are sub-grouped into four molecular subgroups, i.e. Wingless (WNT), Sonic Hedgehog (SHH), Group 3, and Group 4. Among all, Group 3 MB (G3MB) is known to be the most aggressive form, with less than 50% five-year survival. G3MB are associated with large-cell/anaplastic (LCA) histology, distinctive methylation profile, amplification of MYC, and isochromosome 17q (i17q). Targeting these high-risk molecular features unique to G3MB has been challenging, necessitating alternative approaches to therapy for G3-MB. One innovative approach is immunotherapy, which is largely impeded by inhibitory immune checkpoints. B7 homolog 3 (B7-H3/CD276), an immunosuppressive immune checkpoint protein and member of B7 superfamily, is significantly enriched in pediatric malignancies of CNS including G3MB. The enhanced expression of B7-H3/CD276 has been associated with aggressive and metastatic potential. B7-H3/CD276 is also a primary target of miR-1253, a novel tumor suppressor gene silenced in G3MB. Using a structure-based drug discovery pipeline, we screened the ChemBridge library of compounds to discover selective B7-H3 small-molecule inhibitors. Selective B7-H3 inhibitors Ni1 and Ni4 exhibited strong binding scores, CNS penetrance, and oral bioavailability. In vitro, both compounds had appreciably low IC50 values of 3µM (Ni1) and 0.75µM (Ni4). Further, both compounds inhibited wound healing and colony formation. Ni1 shifted the thermostability of B7-H3, suggesting in vitro biding. Ni1 has also undergone PK/PD and MTD studies in vivo, showing stability in serum, good blood-brain barrier permeability, and a half-life of 8 hours. We are now elucidating B7-H3-activated downstream signaling through JAK2/STAT3 signaling and testing the in vivo efficacy for Ni1 against G3MB tumors in a murine model.
Mental health in Europe during the COVID-19 pandemic: a systematic review
Authors: Nafiso Ahmed, Phoebe Barnett, Anna Greenburgh, Tamara Pemovska, Theodora Stefanidou, Natasha Lyons, Sarah Ikhtabi, Shivangi Talwar, Emma R Francis, Samantha M Harris, Prisha Shah, Karen Machin, Stephen Jeffreys, Lizzie Mitchell, Chris Lynch, Una Foye, Merle Schlief, Rebecca Appleton, Katherine R K Saunders, Helen Baldwin, Sophie M Allan, Luke Sheridan-Rains, Omaya Kharboutly, Ariana Kular, Peter Goldblatt, Robert Stewart, James B Kirkbride, Brynmor Lloyd-Evans, Sonia Johnson
Journal: The Lancet Psychiatry (2023)
MDB-27. A PRO-DRUG OF TRIPTOLIDE IN CLINICAL DEVELOPMENT ATTENUATES HIGH-RISK MEDULLOBLASTOMA GROWTH
Authors: Jezabel Rodriguez-Blanco, April Salvador, Robert Suter, Isabel Palomo-Caturla, Megan Viera, Ashley Metts Nienhius, Nagi Ayad, David Robbins
Journal: Neuro-Oncology (2023)

Abstract Medulloblastoma (MB), the most common malignant brain tumor of childhood, is currently classified in four major subgroups. A natural compound used in Chinese medicine for centuries, triptolide, has been shown to have a potent antitumor activity, and the efficacy of one of its derivatives is being evaluated in the clinic. However, to date no preclinical data supports the use of triptolide for the treatment of patients with MB. Here, we performed bioinformatic analyses to predict which subgroup of medulloblastoma patients would more likely benefit from the use of triptolide, and validated its efficacy in series of ex vivo and in vivo mouse and human derived MB models. Correlation analyses identified Group 3 (G3) MB patients as the most prone to respond to triptolide treatment. Consistent with this prediction, triptolide attenuated the growth of G3 MB at lower doses than those classified as SHH subgroup, increasing symptom-free survival in G3 mouse MB models. Transcriptomic analyses revealed MYC signaling as the key downstream target of triptolide in MB cells. Importantly, a pro-drug of triptolide in clinical development, minnelide, similarly showed efficacy in mouse and human derived G3 in vivo MB models. Our findings highlight the potential of repurposing Minnelide to treat G3 MB patients. Due to their dismal prognosis, inclusion of G3 MB patients in future minnelide clinical trials should be considered.
EPEN-02. OPTIMISING BIOMARKERS FOR ACCURATE EPENDYMOMA DIAGNOSIS, PROGNOSTICATION AND STRATIFICATION WITHIN INTERNATIONAL CLINICAL TRIALS: A BIOMECA STUDY
Authors: Rebecca J Chapman, David R Ghasemi, Felipe Andreiuolo, Valentina Zschernack, Arnault Tauziede Espariat, Francesca Buttarelli, Felice Giangaspero, Jacques Grill, Christine Haberler, Simon M L Paine, Ian Scott, Thomas S Jacques, Martin Sill, Pfister Stephan, John Paul Kilday, Pierre LeBlond, Maura Massimino, Piergiorgio Modena, Pascale Varlet, Torsten Pietsch, Richard G Grundy, Kristian W Pajtler, Timothy A Ritzmann
Journal: Neuro-Oncology (2023)

Abstract Accurate identification of brain tumour molecular subgroups is increasingly important. We aimed to establish the most accurate and reproducible ependymoma subgroup biomarker detection techniques, across 147 cases from International Society of Pediatric Oncology (SIOP) Ependymoma II trial participants, enrolled in the pan-European “Biomarkers of Ependymoma in Children and Adolescents (BIOMECA)” study. Across six European BIOMECA laboratories we evaluated epigenetic profiling (DNA methylation array); immunohistochemistry (IHC) for nuclear p65-RELA, H3K27me3, and Tenascin-C; copy number analysis via FISH and MLPA (1q, CDKN2A), and MIP and DNA methylation array (genome-wide copy number evaluation); analysis of ZFTA- and YAP1-fusions by RT-PCR and sequencing, Nanostring and break-apart FISH. DNA Methylation profiling classified 65.3% (n=96/147) of cases as EPN-PFA and 15% (n=22/147) as ST-ZFTA fusion-positive. Immunohistochemical loss of H3K27me3 was a reproducible and accurate surrogate marker for EPN-PFA (sensitivity 99-100% across three centres). IHC for p65-RELA, FISH, and RNA-based analyses effectively identified ZFTA- and YAP1- fused supratentorial ependymomas. Detection of 1q gain using FISH exhibited only 57% inter-centre concordance and low sensitivity and specificity whilst MIP, MLPA and DNA methylation-based approaches demonstrated greater accuracy. We confirm, in a prospective trial cohort, that H3K27me3 IHC is a robust EPN-PFA biomarker. Tenascin-C should be abandoned as a PFA marker. DNA methylation and MIP arrays are effective tools for copy number analysis of 1q gain, 6q and CDKN2A loss whilst FISH is inadequate. Fusion detection was successful, but rare novel fusions need more extensive technologies. We propose CORE and CORE Plus test sets to guide future diagnostic approaches. CORE tests represent those that can currently be used to stratify and inform clinical trials and diagnosis and include IHC and DNA methylation profiling. CORE Plus tests have additional advantages for challenging cases and for use in the research setting and comprise of MIP and RNA-NGS sequencing.
OTHR-09. A RETROSPECTIVE COHORT STUDY EXAMINING RADIOLOGIC AND CLINICAL CHARACTERISTICS OF CHILDREN AND ADOLESCENTS WITH ATYPICAL/COMPLEX PINEAL CYSTS
Authors: Meghan Tahbaz, Jemily Malvar, Sara Khan, Benita Tamrazi, Yueh-Yun Chi, Nathan Robison
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION The significance of atypical or complex pineal cysts (CPC) on magnetic resonance imaging (MRI) is often unclear, and the appropriate management has not been well defined. We conducted a retrospective cohort study of children and adolescents (0-18 years of age) with complex pineal cysts noted on brain MRIs obtained at Children’s Hospital Los Angeles (CHLA) prior to 05/31/2022. METHODS We retrospectively reviewed electronic medical records at CHLA to identify patients &amp;lt;18 years of age who were diagnosed with CPC upon MRI between January 1, 2010 and May 31, 2022. CPC were defined as cysts that are multi-cystic, enhancing, ≥1 cm in size, have a solid component, or exhibit restricted diffusion. Patients were identified by an automated Boolean search of a radiology report database; individual reports were then reviewed for eligibility. Patients with normal pineal glands or simple (&amp;lt;1 cm) pineal cysts were excluded. Electronic medical records were evaluated for patient chief complaint, initial clinical and radiographic symptoms, tumor markers (beta-human chorionic gonadotropin and alpha-fetoprotein), and final diagnosis. RESULTS We identified a cohort of 175 patients; 106 (61%) were female. Mean age at initial MRI was 8.36 years of age (SD 5.36). Tumor markers were measured in 52 patients (30%). The most common presenting symptoms for patients were headache (34%), seizures (26%), nausea/vomiting (19%), weakness/fatigue (17%), and dizziness (12%). Additional presenting symptoms included ataxia, sensory changes, and anxiety. Pineal malignancies were identified in 4 patients (2.2%), which consisted of a pituitary pure germinoma, a pineal region parenchymal tumor, and two pineoblastomas. The remaining 98% of patients (171 patients) either had a benign pineal cyst or were categorized as unknown. CONCLUSION Most CPC are not associated with malignant neoplasms and represent incidental findings with scant clinical significance.
DIPG-15. CONCURRENT GB-13 (IL13.E13K-PE4E) IMPROVES THE EFFICACY OF RADIATION THERAPY IN DIFFUSE INTRINSIC PONTINE GLIOMA
Authors: Julian S Rechberger, Randy S Schrecengost, Liang Zhang, Jizhi Ge, Leo F Nonnenbroich, Jann N Sarkaria, David J Daniels
Journal: Neuro-Oncology (2023)

Abstract Diffuse midline glioma with H3 K27 alterations (DMG) is the most aggressive primary malignant brain tumor in the pediatric population. Radiation therapy (RT) is the standard-of-care; however, it has not demonstrated a significant improvement in overall survival or stalled disease progression, and children usually succumb to disease within 12-15 months of diagnosis. Consequently, finding efficient treatments for DMG remains one of the most critical unmet needs in modern neuro-oncology. Interleukin 13 receptor subunit alpha 2 (IL-13Rα2) is a cell-surface receptor upregulated in ~80% of DMG versus normal brain, posing a potentially promising therapeutic target. Immunotherapies harnessing IL-13Rα2 to selectively delivery cytotoxic payloads, such as pseudomonas exotoxin A (PE), to tumor cells have been previously demonstrated to be safe in DMG patients and efficacious in preclinical models of DMG with high IL-13Rα2 expression using convection-enhanced delivery (CED). Furthermore, there is evidence that PE-based therapies can sensitize cells to RT. In this study, we utilized in vitro and in vivo models of DMG to evaluate clinically-relevant combination treatments of RT and the IL-13/PE immunotoxin GB-13 (IL13.E13K-PE4E). GB-13 improved the effectiveness of low-dose RT in multiple DMG cell lines by promoting caspase activation, which boosted apoptotic cell death. Intratumoral administration of GB-13 via chronic CED decreased tumor burden and prolonged survival in both DMG patient-derived orthotopic xenograft and genetically engineered mouse models. When GB-13 and RT were administered concurrently, this impact became even more prominent, informing future preclinical and clinical investigation of a potentially efficacious therapeutic approach in a subset of DMG.
BIOL-23. LOSS OF MICRORNAS COOPERATES WITH TUMOR SUPPRESSORS TO INITIATE MYC-DEPENDENT METASTATIC MEDULLOBLASTOMA
Authors: Sheila Alcantara Llaguno, Inga Nazarenko, Yuntao Chen, Daochun Sun, Brian Gudenas, Olivier Saulnier, Gaspare La Rocca, Alicia Pedraza, Dennis Burns, Tejus Bale, Andrea Ventura, Paul Northcott, Michael Taylor, Luis Parada
Journal: Neuro-Oncology (2023)

Abstract To determine the role of microRNA regulation in brain tumor development, we incorporated a conditional allele of the microRNA processing enzyme Dicer to a glioma mouse model based on inactivation of the tumor suppressors Nf1, Trp53, and Pten using the Nestin-creERT2 transgene. Loss of Dicer and tumor suppressors at adult ages led to glioma development; however, mutant mice tamoxifen induced at early postnatal ages developed medulloblastoma (MB) instead of glioma. The switch in tumor spectrum occurred with 100% penetrance and the cerebellar tumors were histologically indistinguishable from human MB. The minimum genetic mutations required for MB formation were Dicer1 and Trp53, while additional loss of Pten produced more invasive tumors with leptomeningeal metastasis. Analysis of tumor transcriptome and MB subtype-specific markers show that Dicer tumors most resemble human Sonic Hedgehog (SHH) MB. The presence of leptomeningeal metastasis, Trp53 loss and upregulation of Mycn and Gli2 in the setting of activated Shh signaling suggests that this model phenocopies extremely high risk p53-mutated SHH MB, which carries poor prognosis and is associated with the majority of treatment failures in SHH MB. Analysis of pre-symptomatic mutant mice showed proliferative defects and retained cells in the external granule cell layer (EGL), suggesting that tumors may arise from cerebellar granule neuron precursors (CGNPs). However, targeting CGNPs using Math1-creERT2 did not lead to MB development, suggesting that an earlier EGL precursor may be required for tumorigenesis. Dicer tumors exhibit reduced microRNAs and RNA-induced silencing complexes consistent with loss of Dicer. One of these downregulated microRNAs, miR-101, is a regulator of Mycn and its overexpression leads to Mycn downregulation and inhibition of MB growth. Likewise, genetic and pharmacologic inhibition of Myc leads to inhibition of MB growth. These studies demonstrate a role for microRNAs in Myc-dependent MB development and show an alternative pathway for SHH MB tumorigenesis.
LGG-03. EXPLORING THE SIGNALING NETWORK INVOLVED IN MAPK PATHWAY INHIBITION BY THE MEK INHIBITOR TRAMETINIB IN BRAF-FUSION-DRIVEN PEDIATRIC PILOCYTIC ASTROCYTOMA
Authors: Romain Sigaud, Anja Stefanski, Florian Selt, Thomas Hielscher, Diren Usta, Daniela Kocher, Daniel Picard, Isabel Büdenbender, Marc Remke, Stefan M Pfister, David T W Jones, Tilman Brummer, Olaf Witt, Till Milde
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION Pilocytic astrocytomas (PA) are the most common pediatric brain tumors. They are characterized by MAPK pathway alterations, leading to its constitutive activation and modulating the balance between proliferation and oncogene-induced senescence (OIS) sustained by senescence-associated secretory phenotype (SASP). Little is known about the molecular implications of MAPK pathway inhibition in the proliferating and senescent tumor compartments. METHODS DKFZ-BT66 cells derived from a primary KIAA:BRAF-fusion positive PA cell line and BT40 cells derived from pleomorphic xanthoastrocytoma with a BRAFV600E mutation and CDKN2A/B deletion, were used as model systems. RNA-sequencing and phospho-/proteomic datasets were generated in both the proliferative and senescent cells, and treated with the MEKi trametinib for different time-spans. A multi-omics factor analysis tool (MEFISTO) was used to identify key OIS/proliferation effectors. RESULTS Differential gene expression analysis revealed that MEK inhibition leads to the inhibition of the OIS/SASP gene program in senescent DKFZ-BT66. In addition, the protein level of several SASP factors was decreased. This translated in reduced sensitivity towards senolytics drugs, indicating inhibition of senescence features upon MEKi. MEFISTO analysis allowed to identify key transcription factors, genes and proteins involved in MAPK-induced OIS in the senescent PA cells, that were mapped using a prior knowledge network approach. Finally, single sample geneset enrichment analysis showed that most MAPK-related signatures were downregulated upon MEKi treatment, while pathways related to upstream MAPK activators (including several RTK pathways) were predicted to be upregulated, in both proliferating and senescent cells. CONCLUSION This data suggests that MAPKi reverses OIS in senescent PA cells, while inducing the activation of MAPK upstream regulators, identifying putative co-targets for the treatment of PA. Further validation of the targetability of these pathways is pending. Furthermore, the identification of the MAPK-related OIS/SASP genes provide insight about the regulation of OIS/SASP by the MAPK pathway.